# BUSCO plots all kmer sets
# setwd("~/Desktop/R/ramon/TransPi/paper/")
library(reshape2)
library(plotly)
library(dplyr)
csv=read.csv("busco3_100.csv", header=TRUE)
Complete
## Complete genes comparison
## [1] "One (or more) set is not normally distributed"
## [1] "Data not significant. Skipping pairwise comparison"
Single
## Single genes comparison
## [1] "One (or more) set is not normally distributed"
## [1] "Kruskal-Wallis test was significant (p<.05)"
##
## Pairwise comparisons using Wilcoxon rank sum test
##
## data: sing$Score and sing$Program
##
## Transpi
## Trinity 6.1e-14
##
## P value adjustment method: BH
Duplicated
## Duplicated genes comparison
## [1] "One (or more) set is not normally distributed"
## [1] "Kruskal-Wallis test was significant (p<.05)"
##
## Pairwise comparisons using Wilcoxon rank sum test
##
## data: dup$Score and dup$Program
##
## Transpi
## Trinity 3.3e-08
##
## P value adjustment method: BH
Fragmented
## Fragmented genes comparison
## [1] "One (or more) set is not normally distributed"
## [1] "Data not significant. Skipping pairwise comparison"
Missing
## Missing genes comparison
## [1] "One (or more) set is not normally distributed"
## [1] "Data not significant. Skipping pairwise comparison"
Only TransPi
Complete
## Complete genes comparison
## [1] "One (or more) set is not normally distributed"
## [1] "Data not significant. Skipping pairwise comparison"
Single
## Single genes comparison
## [1] "One (or more) set is not normally distributed"
## [1] "Data not significant. Skipping pairwise comparison"
Duplicated
## Duplicated genes comparison
## [1] "One (or more) set is not normally distributed"
## [1] "Data not significant. Skipping pairwise comparison"
Fragmented
## Fragmented genes comparison
## [1] "One (or more) set is not normally distributed"
## [1] "Data not significant. Skipping pairwise comparison"
Missing
## Missing genes comparison
## [1] "One (or more) set is not normally distributed"
## [1] "Data not significant. Skipping pairwise comparison"
Complete
## Complete genes comparison
## [1] "One (or more) set is not normally distributed"
## [1] "Data not significant. Skipping pairwise comparison"
Single
## Single genes comparison
## [1] "All sets are normally distributed"
## [1] "ANOVA"
## Df Sum Sq Mean Sq F value Pr(>F)
## Kmer 2 0.8 0.38 0.004 0.996
## Residuals 33 2862.0 86.73
## [1] "Pairwise comparison"
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = Score ~ Kmer, data = ceTra2)
##
## $Kmer
## diff lwr upr p adj
## KmerB-KmerA -0.33333333 -9.662397 8.995731 0.9957715
## KmerC-KmerA -0.27500000 -9.604064 9.054064 0.9971199
## KmerC-KmerB 0.05833333 -9.270731 9.387397 0.9998702
Duplicated
## Duplicated genes comparison
## [1] "All sets are normally distributed"
## [1] "ANOVA"
## Df Sum Sq Mean Sq F value Pr(>F)
## Kmer 2 0.6 0.31 0.009 0.991
## Residuals 33 1138.3 34.49
## [1] "Pairwise comparison"
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = Score ~ Kmer, data = ceTra2)
##
## $Kmer
## diff lwr upr p adj
## KmerB-KmerA 0.3166667 -5.566869 6.200203 0.9904328
## KmerC-KmerA 0.2000000 -5.683536 6.083536 0.9961719
## KmerC-KmerB -0.1166667 -6.000203 5.766869 0.9986956
Fragmented
## Fragmented genes comparison
## [1] "One (or more) set is not normally distributed"
## [1] "Data not significant. Skipping pairwise comparison"
Missing
## Fragmented genes comparison
## [1] "All sets are normally distributed"
## [1] "ANOVA"
## Df Sum Sq Mean Sq F value Pr(>F)
## Kmer 2 0 0.002 0 1
## Residuals 33 246 7.455
## [1] "Pairwise comparison"
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = Score ~ Kmer, data = ceTra2)
##
## $Kmer
## diff lwr upr p adj
## KmerB-KmerA 0.025000000 -2.710109 2.760109 0.9997227
## KmerC-KmerA 0.016666667 -2.718442 2.751776 0.9998767
## KmerC-KmerB -0.008333333 -2.743442 2.726776 0.9999692
BUSCO and reads
## comp.Program comp.Category comp.Score comp.Reads comp.Sample
## 1 Transpi Complete 82.3 49,743,412 CE1
## 2 Transpi Complete 82.3 38,836,876 CE2
## 3 Transpi Complete 67.1 11,166,310 CE3
## 4 Transpi Complete 80.4 11,626,153 CE4
## 5 Transpi Complete 85.3 12,567,755 CE5
## 6 Transpi Complete 69.6 14,372,593 CE6
Complete
## Complete genes comparison
## [1] "All sets are normally distributed"
## [1] "ANOVA"
## Df Sum Sq Mean Sq F value Pr(>F)
## Kmer 2 0.112 0.0558 0.084 0.92
## Residuals 33 21.968 0.6657
## [1] "Pairwise comparison"
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = Score ~ Kmer, data = dmTra2)
##
## $Kmer
## diff lwr upr p adj
## KmerB-KmerA 0.04166667 -0.7756760 0.8590093 0.9914127
## KmerC-KmerA 0.13333333 -0.6840093 0.9506760 0.9156942
## KmerC-KmerB 0.09166667 -0.7256760 0.9090093 0.9591627
Single
## Single genes comparison
## [1] "One (or more) set is not normally distributed"
## [1] "Data not significant. Skipping pairwise comparison"
Duplicated
## Duplicated genes comparison
## [1] "One (or more) set is not normally distributed"
## [1] "Data not significant. Skipping pairwise comparison"
Fragmented
## Fragmented genes comparison
## [1] "All sets are normally distributed"
## [1] "ANOVA"
## Df Sum Sq Mean Sq F value Pr(>F)
## Kmer 2 0.037 0.01861 0.179 0.837
## Residuals 33 3.439 0.10422
## [1] "Pairwise comparison"
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = Score ~ Kmer, data = dmTra2)
##
## $Kmer
## diff lwr upr p adj
## KmerB-KmerA 0.01666667 -0.3067275 0.3400609 0.9912244
## KmerC-KmerA -0.05833333 -0.3817275 0.2650609 0.8979782
## KmerC-KmerB -0.07500000 -0.3983942 0.2483942 0.8373956
Missing
## Missing genes comparison
## [1] "All sets are normally distributed"
## [1] "ANOVA"
## Df Sum Sq Mean Sq F value Pr(>F)
## Kmer 2 0.037 0.0186 0.05 0.952
## Residuals 33 12.386 0.3753
## [1] "Pairwise comparison"
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = Score ~ Kmer, data = dmTra2)
##
## $Kmer
## diff lwr upr p adj
## KmerB-KmerA -0.05833333 -0.6720504 0.5553838 0.9704847
## KmerC-KmerA -0.07500000 -0.6887171 0.5387171 0.9517128
## KmerC-KmerB -0.01666667 -0.6303838 0.5970504 0.9975550
BUSCO and reads
## comp.Program comp.Category comp.Score comp.Reads comp.Sample
## 1 Transpi Complete 95.4 30,515,068 DM1
## 2 Transpi Complete 95.8 24,284,630 DM2
## 3 Transpi Complete 95.0 24,773,404 DM3
## 4 Transpi Complete 95.6 30,140,704 DM4
## 5 Transpi Complete 94.6 25,828,680 DM5
## 6 Transpi Complete 95.2 19,049,236 DM6
Complete
## Complete genes comparison
## [1] "One (or more) set is not normally distributed"
## [1] "Data not significant. Skipping pairwise comparison"
Single
## Single genes comparison
## [1] "One (or more) set is not normally distributed"
## [1] "Data not significant. Skipping pairwise comparison"
Duplicated
## Duplicated genes comparison
## [1] "One (or more) set is not normally distributed"
## [1] "Data not significant. Skipping pairwise comparison"
Fragmented
## Fragmented genes comparison
## [1] "One (or more) set is not normally distributed"
## [1] "Data not significant. Skipping pairwise comparison"
Missing
## Missing genes comparison
## [1] "One (or more) set is not normally distributed"
## [1] "Data not significant. Skipping pairwise comparison"
BUSCO and reads
## comp.Program comp.Category comp.Score comp.Reads comp.Sample
## 1 Transpi Complete 96.3 182,180,123 MM1
## 2 Transpi Complete 97.0 107,280,600 MM2
## 3 Transpi Complete 97.3 127,017,374 MM3
## 4 Transpi Complete 97.3 102,909,165 MM4
## 5 Transpi Complete 97.3 65,372,078 MM5
## 6 Transpi Complete 53.9 27,016,597 MM6